Primary change is HDFFV-11212 - new refs and JNI (#372)

* OESS-98 convert plugin option to FetchContent, add tests

* Fixes for pkcfg files because of plugin option

* OESS-98 fix tools test for plugins

* Keep doxygen comments under 100 chars long - format hint

* Whitespace

* HDFFV-11144 - Reclassify CMake messages

* HDFFV-11099/11100 added help text

* Reworked switch statement to compare string instead

* Fix typo

* Update CDash mode

* Correct name of threadsafe

* Correct option name

* Undo accidental commit

* Note LLVM 10 to 11 format default changes

* Update format plugin

* Undo clang-format version 11 changes

* One more correction

* Update supported platforms

* Revert whitespace changes

* Correct whitespace

* Changes from PR#3

* HDFFV-11213 added option to control gcc10 warnings diagnostics

* HDFFV-11212 Use the new references correctly in JNI utility and tests

* format source

* Fix typo

* Add new test file

* HDFFV-11212 - update test and remove unused arg

* Minor non-space formatting changes

* Use H5I_INVALID_ID instead of "-1"

* source formatting

* add missing testfile, update jni function

* Undo commit of debug code

* remove mislocated file

* Fix h5repack test for handling of fapls and id close

* Update h5diff test files usage text

* HDFFV-11212 add new ref tests for JNI export dataset

* src format update

* Remove blank line typo

* src format typo

* long double requires %Lg

* Another long double foramt specifer S.B. %Lg

* issue with t128bit test

* Windows issue with h5dump and type.

* Fix review issues

* refactor function nesting and fix error checks

* format fixes

* Remove untested functions and javadoc quiet comments

* Restore TRY block.

* Change string append errors to memory exception

* revert to H5_JNI_FATAL_ERROR - support functions need work

* Add assertion error for h5util functions

* remove duplicate function

* format fix

* Revert HD function error handling

* Update copyright comments

8 files changed, 20 insertions, 20 deletions

diff --git a/java/examples/groups/H5Ex_G_Compact.java b/java/examples/groups/H5Ex_G_Compact.java
index 6078c6c..a24ed33 100644
--- a/java/examples/groups/H5Ex_G_Compact.java
+++ b/java/examples/groups/H5Ex_G_Compact.java
@@ -60,9 +60,9 @@ public class H5Ex_G_Compact {
     }
 
     public static void CreateGroup() {
-        long file_id = -1;
-        long group_id = -1;
-        long fapl_id = -1;
+        long file_id = HDF5Constants.H5I_INVALID_HID;
+        long group_id = HDF5Constants.H5I_INVALID_HID;
+        long fapl_id = HDF5Constants.H5I_INVALID_HID;
         H5G_info_t ginfo;
         long size;
 
diff --git a/java/examples/groups/H5Ex_G_Corder.java b/java/examples/groups/H5Ex_G_Corder.java
index 74f70ba..a00252f 100644
--- a/java/examples/groups/H5Ex_G_Corder.java
+++ b/java/examples/groups/H5Ex_G_Corder.java
@@ -25,10 +25,10 @@ public class H5Ex_G_Corder {
     private static String FILE = "H5Ex_G_Corder.h5";
 
     private static void CreateGroup() throws Exception {
-        long file_id = -1;
-        long group_id = -1;
-        long subgroup_id = -1;
-        long gcpl_id = -1;
+        long file_id = HDF5Constants.H5I_INVALID_HID;
+        long group_id = HDF5Constants.H5I_INVALID_HID;
+        long subgroup_id = HDF5Constants.H5I_INVALID_HID;
+        long gcpl_id = HDF5Constants.H5I_INVALID_HID;
         int status;
         H5G_info_t ginfo;
         int i;
diff --git a/java/examples/groups/H5Ex_G_Create.java b/java/examples/groups/H5Ex_G_Create.java
index f653987..7d9e150 100644
--- a/java/examples/groups/H5Ex_G_Create.java
+++ b/java/examples/groups/H5Ex_G_Create.java
@@ -25,8 +25,8 @@ public class H5Ex_G_Create {
     private static String GROUPNAME = "G1";
 
     private static void CreateGroup() {
-        long file_id = -1;
-        long group_id = -1;
+        long file_id = HDF5Constants.H5I_INVALID_HID;
+        long group_id = HDF5Constants.H5I_INVALID_HID;
 
         // Create a new file using default properties.
         try {
diff --git a/java/examples/groups/H5Ex_G_Intermediate.java b/java/examples/groups/H5Ex_G_Intermediate.java
index 6109e9a..4649741 100644
--- a/java/examples/groups/H5Ex_G_Intermediate.java
+++ b/java/examples/groups/H5Ex_G_Intermediate.java
@@ -31,9 +31,9 @@ public class H5Ex_G_Intermediate {
 
     private void CreateGroup() throws Exception {
 
-        long file_id = -1;
-        long group_id = -1;
-        long gcpl_id = -1;
+        long file_id = HDF5Constants.H5I_INVALID_HID;
+        long group_id = HDF5Constants.H5I_INVALID_HID;
+        long gcpl_id = HDF5Constants.H5I_INVALID_HID;
 
         try {
             // Create a new file_id using the default properties.
diff --git a/java/examples/groups/H5Ex_G_Iterate.java b/java/examples/groups/H5Ex_G_Iterate.java
index 71361f8..02798eb 100644
--- a/java/examples/groups/H5Ex_G_Iterate.java
+++ b/java/examples/groups/H5Ex_G_Iterate.java
@@ -58,7 +58,7 @@ public class H5Ex_G_Iterate {
     }
 
     private static void do_iterate() {
-        long file_id = -1;
+        long file_id = HDF5Constants.H5I_INVALID_HID;
 
         // Open a file using default properties.
         try {
diff --git a/java/examples/groups/H5Ex_G_Phase.java b/java/examples/groups/H5Ex_G_Phase.java
index 7824123..744ce6c 100644
--- a/java/examples/groups/H5Ex_G_Phase.java
+++ b/java/examples/groups/H5Ex_G_Phase.java
@@ -60,11 +60,11 @@ public class H5Ex_G_Phase {
     }
 
     private static void CreateGroup() {
-        long file_id = -1;
-        long group_id = -1;
-        long subgroup_id = -1;
-        long fapl_id = -1;
-        long gcpl_id = -1;
+        long file_id = HDF5Constants.H5I_INVALID_HID;
+        long group_id = HDF5Constants.H5I_INVALID_HID;
+        long subgroup_id = HDF5Constants.H5I_INVALID_HID;
+        long fapl_id = HDF5Constants.H5I_INVALID_HID;
+        long gcpl_id = HDF5Constants.H5I_INVALID_HID;
         H5G_info_t ginfo;
         String name = "G0"; // Name of subgroup_id
         int i;
diff --git a/java/examples/groups/H5Ex_G_Traverse.java b/java/examples/groups/H5Ex_G_Traverse.java
index 76ed6c8..61f2122 100644
--- a/java/examples/groups/H5Ex_G_Traverse.java
+++ b/java/examples/groups/H5Ex_G_Traverse.java
@@ -43,7 +43,7 @@ public class H5Ex_G_Traverse {
     public static H5L_iterate_t iter_cb = new H5L_iter_callbackT();
 
     private static void OpenGroup() {
-        long file_id = -1;
+        long file_id = HDF5Constants.H5I_INVALID_HID;
         H5O_info_t infobuf;
         opdata od = new opdata();
 
diff --git a/java/examples/groups/H5Ex_G_Visit.java b/java/examples/groups/H5Ex_G_Visit.java
index c479259..544cbf4 100644
--- a/java/examples/groups/H5Ex_G_Visit.java
+++ b/java/examples/groups/H5Ex_G_Visit.java
@@ -47,7 +47,7 @@ public class H5Ex_G_Visit {
 
     private void VisitGroup() throws Exception {
 
-        long file_id = -1;
+        long file_id = HDF5Constants.H5I_INVALID_HID;
 
         try {
             // Open file